---
title: "Reference Genome"
author: "Pierre Barry"
date: "`r format(Sys.time(), '%d %B, %Y, %H:%M')`"
output: 
  flexdashboard::flex_dashboard:
    theme: paper
    orientation: rows
    social: menu
    source_code: embed
    vertical_layout: scroll
---

```{r global, include=FALSE}
list.of.packages <- c("RColorBrewer","formattable","kableExtra","ggplot2","plotly","png")

for (i in list.of.packages){
  if (i %in% installed.packages()[,"Package"] == FALSE){
    install.packages(i)
  }
  eval(bquote(library(.(i))))
}
```

```{r, include = FALSE}
color_med_atl=data.frame(Location=c("Gulf of Lion","Costa Calida","Algarve","Bay of Biscay"),
                         Col=brewer.pal(n = 4, name = "RdBu"))
```

Reference genome {data-icon="fa-keyboard-o"}
=======================================================================

```{r}
distri_length_reference_genome=vector('list',length(list.files(paste(path,"/data/reference_genome/",sep=""))))
for (i in 1:length(list.files(paste(path,"/data/reference_genome/",sep="")))){
  a<-read.table(paste(paste(path,"/data/reference_genome/",sep=""),list.files(paste(path,"/data/reference_genome/",sep=""))[i],sep=""))
  a<-a[,1]
  distri_length_reference_genome[[i]]=a
}
names(distri_length_reference_genome)=list.files(paste(path,"/data/reference_genome/",sep=""))
sp=list.files(paste(path,"/data/reference_genome/",sep=""))

length_distri=data.frame(Species=c(NA),
                         Num=c(NA),
                         length=c(NA))
for (i in 1:length(sp)){
  
  data_tmp=data.frame(Species=rep(sp[i],length(distri_length_reference_genome[[i]])),
                      Num=seq(1,length(distri_length_reference_genome[[i]])),
                      length=distri_length_reference_genome[[i]])
  
  length_distri=rbind(length_distri,
                      data_tmp)
  
}

length_distri=length_distri[-1,]

mean_length=c()
number_scaff=c()
for (i in 1:length(levels(factor(length_distri$Species)))){
  mean_length[i]=mean(length_distri$length[length_distri$Species==levels(factor(length_distri$Species))[i]])
  number_scaff[i]=length(length_distri$length[length_distri$Species==levels(factor(length_distri$Species))[i]])
}
names(mean_length)=levels(factor(length_distri$Species))
names(number_scaff)=levels(factor(length_distri$Species))

DATA_REFERENCE_GENOME=data.frame(Species=names(mean_length),
                                 Mean_length=as.vector(mean_length)/1000,
                                 Number_scaffold=as.vector(number_scaff))

ref_table=data.frame(NAME=c("0-1e+4",
                            "1e+4-1e+5",
                            "1e+5-1e+6",
                            "1e+6-1e+7",
                            "1e+7-1e+8"),
                     MIN=c(0,1e+4,1e+5,1e+6,1e+7),
                     MAX=c(1e+4,1e+5,1e+6,1e+7,1e+8))


tmp=ifelse(length_distri$length < 1e+4, "0-1e+4", length_distri$length)
tmp=ifelse(length_distri$length >= 1e+4 & length_distri$length<1e+5, "1e+4-1e+5", tmp)
tmp=ifelse(length_distri$length >= 1e+5 & length_distri$length<1e+6, "1e+5-1e+6", tmp)
tmp=ifelse(length_distri$length >= 1e+6 & length_distri$length<1e+7, "1e+6-1e+7", tmp)
tmp=ifelse(length_distri$length >= 1e+7 & length_distri$length<1e+8, "1e+7-1e+8", tmp)

length_distri$group=tmp


DATA_REFERENCE_GENOME$Mean_length <- color_bar("lightgreen")(DATA_REFERENCE_GENOME$Mean_length)
DATA_REFERENCE_GENOME$Number_scaffold <- color_bar("lightgreen")(DATA_REFERENCE_GENOME$Number_scaffold)

DATA_REFERENCE_GENOME$Species = c("Atherina boyeri",
                             "Coryphoblennius galerita",
                             "Coris julis",
                             "Dicentrarchus labrax",
                             "Diplodus puntazzo",
                             "Engraulis encrasicolus",
                             "Gobius niger",
                             "Hippocampus guttulatus",
                             "Lophius budegassa",
                             "Lithognathus mormyrus",
                             "Merluccius merluccius",
                             "Mullus surmuletus",
                             "Pagellus erythrinus",
                             "Serranus cabrilla",
                             "Spondyliosoma cantharus",
                             "Symphodus cinereus",
                             "Sardina pilchardus",
                             "Sarda sarda",
                             "Syngnathus typhle")
```

Row {.tabset}
-----------------------------------------------------------------------

### Table

```{r, fig.height=75}
DATA_REFERENCE_GENOME$Species = cell_spec(DATA_REFERENCE_GENOME$Species,italic = T)

kbl(DATA_REFERENCE_GENOME,col.names = c("Species",
                           "Mean scaffold length (kbp)",
                           "Number of scaffolds")
    ,escape = F,align=c(rep('c',times=2))) %>%
  kable_classic ("striped","hover",full_width = T,html_font = "Cambria")  %>%
  kable_paper("hover", full_width = F) %>%
  column_spec(1, width = "10cm") %>%
  column_spec(2, width = "10cm") %>%
  column_spec(3, width = "7.5cm")
```

### Distribution 

```{r, fig.height=75}
p<-ggplot(length_distri,aes(x=length,fill=group))+
  geom_histogram(alpha=0.5,col="darkblue",bins=200)+
  scale_color_viridis_d()+
  theme_classic()+
  xlab("Length")+
  ylab("Frequency")+
  scale_x_log10()+
  scale_y_log10()+
  facet_grid(Species ~ .)+
  theme(strip.background = element_rect(fill="white"),
        strip.text.y = element_text(size=12, color="darkblue",
                                    face="bold"))+
  scale_fill_viridis_d()

ppp<-ggplotly(p,height=5000)  %>% partial_bundle() %>% hide_legend()

img1<-readPNG(paste(path,"/figures/fish/","Aboye",".png",sep=""))
img3<-readPNG(paste(path,"/figures/fish/","Cgale",".png",sep=""))
img4<-readPNG(paste(path,"/figures/fish/","Cjuli",".png",sep=""))
img5<-readPNG(paste(path,"/figures/fish/","Dlabr",".png",sep=""))
img6<-readPNG(paste(path,"/figures/fish/","Dpunt",".png",sep=""))
img7<-readPNG(paste(path,"/figures/fish/","Eencr",".png",sep=""))
img8<-readPNG(paste(path,"/figures/fish/","Gnige",".png",sep=""))
img9<-readPNG(paste(path,"/figures/fish/","Hgutt",".png",sep=""))
img10<-readPNG(paste(path,"/figures/fish/","Lbude",".png",sep=""))
img11<-readPNG(paste(path,"/figures/fish/","Lmorm",".png",sep=""))
img12<-readPNG(paste(path,"/figures/fish/","Mmerl",".png",sep=""))
img13<-readPNG(paste(path,"/figures/fish/","Msurm",".png",sep=""))
img14<-readPNG(paste(path,"/figures/fish/","Peryt",".png",sep=""))
img15<-readPNG(paste(path,"/figures/fish/","Scabr",".png",sep=""))
img16<-readPNG(paste(path,"/figures/fish/","Scant",".png",sep=""))
img17<-readPNG(paste(path,"/figures/fish/","Scine",".png",sep=""))
img18<-readPNG(paste(path,"/figures/fish/","Spilc",".png",sep=""))
img19<-readPNG(paste(path,"/figures/fish/","Ssard",".png",sep=""))
img20<-readPNG(paste(path,"/figures/fish/","Styph",".png",sep=""))
start=0
end=0.95
vv<-seq(start,end,length.out=20)
vv[19]=0.75
yy<-seq(0.98,0.03,length.out=19)
size.x=0.075
ppp<-  ppp %>%
  layout(
    images = list(
      list(
        source = raster2uri(as.raster(img1)),
        x = vv[19], y = yy[1], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img3)),
        x = vv[19], y = yy[2], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img4)),
        x = vv[19], y = yy[3], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img5)),
        x = vv[19], y = yy[4], 
        sizex = size.x, sizey = 0.05
      ),
      list(
        source = raster2uri(as.raster(img6)),
        x = vv[19], y = yy[5], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img7)),
        x = vv[19], y = yy[6], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img8)),
        x = vv[19], y = yy[7], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img9)),
        x = vv[19], y = yy[8], 
        sizex = size.x, sizey = 0.025
      ),
      list(
        source = raster2uri(as.raster(img10)),
        x = vv[19], y = yy[9], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img11)),
        x = vv[19], y = yy[10], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img12)),
        x = vv[19], y = yy[11], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img13)),
        x = vv[19], y = yy[12], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img14)),
        x = vv[19],y = yy[13], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img15)),
        x = vv[19], y = yy[14], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img16)),
        x = vv[19], y = yy[15], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img17)),
        x = vv[19], y = yy[16], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img18)),
        x = vv[19], y = yy[17], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img19)),
        x = vv[19], y = yy[18], 
        sizex = size.x, sizey = 0.1
      ),
      list(
        source = raster2uri(as.raster(img20)),
        x = vv[19], y = yy[19], 
        sizex = size.x, sizey = 0.1
      )
    )
  ) 
ppp
```

Packages used {data-icon="fa-map"}
=======================================================================

```{r}
installed.packages()[names(sessionInfo()$otherPkgs), "Version"]
```